


Captive Captain

by orphan_account



Category: Star Trek
Genre: Alpha Khan, Alpha/Beta/Omega Dynamics, Dubious Consent, Knotting, M/M, Mpreg, Non-Consensual Drug Use, OOC, Omega Kirk, forced relationships - Freeform, younger Kirk
Language: English
Status: In-Progress
Published: 2016-08-06
Updated: 2016-08-20
Packaged: 2018-07-29 19:05:42
Rating: Mature
Warnings: Rape/Non-Con
Chapters: 8
Words: 8,866
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/7695826
Author URL: https://archiveofourown.org/users/orphan_account/pseuds/orphan_account
Summary: <blockquote class="userstuff">
              <p>Khan and Kirk are kidnapped by scientists and forced to breed.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> Yeah so I posted this about a year ago but it felt rushed and I didn't like it so I'm trying again.

Chapter 1  
Drugs. It was like fire and ice fought within him. He was lust. He was rage. A scent of sex and relief from pain called to him relentlessly. Enticed him. There was grunting and screaming but none of it he heard for very long. There was crying and pleasure. Oh, so much pleasure. There was a shock of brilliance and a climax that was ecstasy. He took his pleasure again and again and again. 

For Kirk he was far more lucid when a raging alpha had stormed into the room. Kirk had been forcibly tied down to the bed by his captors in anticipation of said alpha. He was already crying and pleading but nothing he said stopped the alpha from 'taking what was his'. There was no love in the act. The alpha tore into him painfully. It had been agony. Over and over the alpha claimed him for what felt like hours. Kirk thought he was going to die. He screamed and screamed and screamed. He passed out and the alpha hit him until he woke up. Kirk pleaded but to no avail. The alpha didn't stop. 

Time passed Kirk didn't know how long but when it was finally, finally over and the alpha got off of him. Kirk fell to the floor with a thud. His thighs and legs unable to support him. He gasped in agony. Unable to hold back a whimper. His head was spinning and his throat was dry. Water, he so desperately needed water. 

When the world felt a little more stable he began crawling towards the bathroom, wanting nothing except to soak his tired body in warm water. He had barely gone a few feet before he slumped against the wall, exhausted and shaking. His body felt warm all of a sudden, almost feverish. His could feel every pound of his heart as it sent boiling blood through his veins. Every breathe felt heavy and controlled. Like if he didn't focus on it it would stop. 

He must have dozed off because he did not hear Khan get out of the bed. The drugs had worn off very quickly leaving little effect on the augment.

A hand touched his forehead, waking him from his hazy sleep in a hurry. His head jerked backwards forcibly as he turned to look at his assailant. Wide and fearful eyes peered up at Khan but the dark man was looking at Kirk's battered body with a look of horror. He kneeled so as not to loom over the trembling young man.

"Did I do this?" Khan asked quietly, reaching out slowly to place a hand on Kirk's badly bruised and fractured hip. The touch was gentle but it still paralyzed Kirk. "Please don't." He gasped. "P–Please. I can't do it again. Please don't. I've never–I just want to go back home. Please. It hurts so much. I can't–please don't."

He closed his legs and drew his knees in and tucked them as far as a fractured hip would let him. He folded his arms defensively over his head. His whole body shaking with repressed sobs. His scent shouted scared, hurt and vulnerable. Khan knew he had to do something. With his augment strength it's possible he could have broken some of the omega's bones. He needed medical attention. Khan rose from his crouch beside him. This was his fault and he was going to do everything he could to fix it. 

Kirk was still quietly sobbing when a light blanket covered up his nakedness and gentle arms lifted him from the cold floor. Kirk seized and struggled as he realized the dark man was carrying him back to the bed. Scared that the man had not heeded his last plea, as a last ditch effort he begged "Just be gentle. Just don't hurt me. Please I hurt so much." He was gasping and crying when all of a sudden his chest tightened and he couldn't breathe. He panicked and tried to lash out. Only causing the arms to hold him tighter. He was truly afraid that Khan was going to hurt him further maybe even kill him because he knew he couldn't escape and there was no way he would survive a round two. 

There was no doubt. In his drugged stupor Khan knew that he had raped and nearly killed the young omega. He couldn't remember any of it but it broke something in Khan to have caused the youth so much distress. Khan mentally face-palmed himself. Of course the boy would be frightened of the bed. He simply wrapped Kirk up tighter in the blanket and sat him upright on the bed, pulling the trembling form into his chest. He felt Kirk's erratic heartbeat through the blanket. His breaths coming in ragged pants. He still struggled weakly. Khan shushed him gently but Kirk was too far gone in his panic to hear him. "Please! I'm sorry! Don't! Please!" 

The augment looped his arm under Kirk's so that he held him up by his chest and began gently rubbing his back in what he hoped was a soothing gesture. 

"You are experiencing a panic attack. Try to calm down. Hush now. You're going to pass out if you don't breathe. Shh. I'm not going to hurt you. You don't have to do anything except calm down. That's it. Shh." Khan cooed. Somewhere he knew he should feel ridiculous for speaking this way but the regret he felt that was deeper than the sea negated any qualms he may had had. 

Kirk's vision had gotten spotty. Desperately he tried to even out his breathing. The warm hand on his back did have a calming effect and served as an anchor. Inhale. Hold. Exhale. Inhale. Hold. Exhale. He kept up this pattern for a long until his heart stopped feeling like it was going to break free of his chest and his chest stopped feeling like it had iron bands squeezing it. After the adrenalin was out of his system Kirk had nothing left. His head drooped onto his chest. Completely exhausted. 

His body was way past it's limits but still he fought sleep. Scared of what might happen to him if he let his guard down. 

"Just make it quick." he whispered. His voice hoarse and pleading.

The augment lifted and turned his head so that it was neatly tucked into his shoulder. Warm arms held him as he heard the deep voice murmur. 

"Not gonna hurt you. Didn't want to hurt you but I'm sorry that I did. I didn't want to." A hand repositioned itself on Kirk's neck. 

"Sleep. Your body needs it. I promise you all will be well. No harm will come to you." 

This time Kirk didn't have the strength to fight it, too exhausted to even nod, his eyes closed and sleep claimed him. 

 

Khan sat in silence for awhile just holding Kirk before he finally lay him down as gently as he could and positioned him on his back in hope it would be easier on his hips and ribs. The kid would need constant supervision. Khan hadn't missed that knock to the head he took and a concussion might not be the worst of his injuries.   
Khan retrieved the first aid kit that he kept on his person for away mission emergencies and took out a standard tricorder. He was no doctor but quick scan revealed that the kid was dehydrated, had four fractured ribs and his hip showed hairline fractures not to mention he was also a mess of bites and bruises. He did not have a concussion though. Khan thanked small mercies. 

Khan hesitated. His medical kit carried a sedative as well as plenty of pain killers. He needed to check the rest of the kid's wounds and he certainly didn't want him awake when he did so but the kid was probably so deeply unconscious that a sedative could possibly kill him. In the end he was able to calculate a dosage small enough for his immune system and weight. His sedatives were designed so that they'd be effective against even an augment's body so he triple checked it. Just in case.

With a slight hiss of the hypospray the deed was done. Khan checked the kid's vital signs. A bit sluggish but otherwise alright. 

From the bathroom he filled a bucket of warm soapy water before positioning a pillow under the omega's hips and turning him onto his stomach. Khan winced in sympathy. Blood trailed down his thighs and blood from love bites marred his shoulders. Khan couldn't help but think of how much it must have hurt the kid. His buttocks and thighs were an ugly purple mess and his arms and wrists were rubbed raw from where he must have struggled. Khan cleaned him up as best he could before stripping the bed and carefully binding the kid's ribs. Having taken care of everything else he washed and dressed himself as well. He would fix this he promised himself.

During the night Khan kept careful watch over Kirk as his temperature increased. Kirk struggled in his fever dreams a few times which sadly forced Khan to restrain him in hopes of preventing further damage. He held the omega down as he strained against him. He whispered assurances mostly for his own sake since he was almost certain the blonde couldn't hear him. During his quiet moments Khan bathed him in cool water. Trying desperately to lower his temperature but having little luck. He was angry. Angry at his captors and angry at himself for falling into such a trap. His alpha instincts took over. 

"You bastards! He's dying! If you wanted us alive to mate so badly the least you can do is keep him alive!" He screamed to his unseen captors. 

Apparently they agreed with him and as soon as the words had left his mouth a team of armoured men flooded into the room. They all carried weapons that went off the moment Khan jumped for them. 

When Khan came to the blond omega had an IV next to his bed and proper gauze around his ribs. As tired as Khan was at being drugged he was pleased the omega had gotten proper medical treatment. Kirk was still feverish but his temperature was lower. Khan caught of whiff of something that made his heart drop to his stomach; the omega had bonded to him. 

Khan inspected the omegas scruff and saw the bondmark. His bondmark. The omega was his mate now. Khan felt so sorry. He'd raped this young man. He'd hurt him and scared him and because of Khan the kid would never want to get naked for anyone else for a long time. This kid's first experience with sex had broken some of his bones. If Khan broke the bond with him now he'd probably kill the boy. 

He could feel it now. At the back of his mind an awareness of the omega blossomed. A tiny bundle of currently unconscious emotions. Khan ran his hand through his hair. "How did this happen?" He asked himself. He sat down and looked over his omega. His omega now. He wouldn't let anyone hurt him anymore. Not even himself. He would make this right. He had to. 

The first time the omega opened his eyes Khan knew he wasn't lucid. His eyes were glassy and looked around seeing nothing. Khan took hold of his hand and pushed feelings of safety and comfort through the bond until he could feel him drift back to sleep. 

The next time he woke the omega panicked. He screamed. He fought to get away but gasped and ceased his struggles only to hiss and shudder in pain. He relaxed somewhat when he realized Khan hadn't moved from his location in the corner of the room.The alpha respectfully kept his distance until he calmed down. He had chosen this spot specifically so as to be within the omega's line of sight but far enough away to not poise a threat. 

Khan pushed comfort and calm through the newly formed bond; trying to communicate through it to his new mate that he wasn't going to hurt him anymore and that he was safe. After awhile the omega calmed down somewhat and Khan stopped feeling his panic so sharply in his own mind. He struggled for the words to say. What do you say to someone in his situation? 

He approached slowly. "I'm going to touch you to help you sit up." Khan warned. The omega didn't respond so Khan carefully slid an arm under him and felt the muscles tense as he shifted him into an upright position. The omega hissed in pain but he downed the entire glass that was on the night stand before he glanced at Khan. Khan noticed the blond was careful not to make eye-contact and kept his head down placatingly. He was still understandably scared of him. He probably thought he would kill him if he wasn't careful. 

He looked so young and scared. He was shaking like a leaf and his scent was sour with fear and submission. Khan knew he needed to say something. When he laid a hand on him the omega jerked violently as if he expected Khan to hit him. The omega's trembling tripled and Khan could smell salt. The omega, still with his head down, was crying silently. Ashamed of his own fear. 

Khan bundled him up and just held him as his omega sobbed. He could feel the kid's pain in his heart. He felt the blond's fear, apprehension, trepidation, shame, guilt, horror and confusion all roll through the bond. All his emotions felt...off. As if he were still asleep. Khan guessed he was still in a deep state of shock. 

Once the blond quieted down Khan began to speak."My name is Khan Noonien Sighn. What is yours?" The omega didn't seem to hear him so Khan asked again. Making sure to speak slowly and clearly. 

The omega jolted and opened his mouth to answer but no words came out. Through the bond Khan sensed more confusion, fear, more shock and growing panic at his question. The omega began to cry again. "Shh. No no It's ok." Khan soothed at the omega's panicked and frighted expression. 

"Sometimes when something traumatic happens to us we get all jumbled up inside. It's alright." Khan didn't know if the omega could understand in the state he was in but Khan continued. "They took me from my family as they have taken you from yours. They drugged me so that I would bond with you. Forgive me, but we have successfully bonded meaning you are now my mate. I didn't mean for this to happen but I promise to treat you as if I had chosen you. I will protect you and keep you safe. I will find a way to get us out of here and get us both home. I do not expect you to forgive my actions but I will try to make amends to you somehow."

"James Tiberius Kirk." The omega whispered in a hoarse and worn out voice.   
"My name is James Tiberius Kirk."


	2. Chapter 2

Chapter 2  
His body hurt. Everything ached in the most humiliating places. He doubted he could walk by himself to the bathroom. 

Kirk was still terrified but after the first day he tried to cover it with an air of bravado. He wasn't scared of Khan per say, more of the realization that their captors could easily drug Khan again and there was nothing he could do to defend himself if that happened. It was the anxiety and helplessness that made him feel sick to his stomach. Kirk did not trust this man-his mate, to protect him. 

He tried not to think about how this man bonded him. He tried his best to smother any emotions he might be sending through the bond but it seemed daunting to try. 

He felt like his emotions were out of control no matter how he tried to rein them in. He tried to put on a brave face but still couldn't make eye-contact with the alpha, still flinched if the alpha moved too quickly and was unable to speak much louder than a hoarse whisper due to his damaged throat. He wanted to cry but felt scared to draw the attention to himself. 

He cursed himself for feeling scared but couldn't stop. He didn't want to be here. He was vulnerable to the whims of a super-human and a league of scientists who didn't seem to care about his survival. They were studying Khan, not him. He was just the toy they threw to the tiger to see how it reacted. 

Kirk hugged his knees and shivered. The room was always cold. Not freezing but always a few degrees under comfortable. Kirk wondered if their captors did it to keep them docile. Animals become sluggish and sleepy when cold. 

Finally he gave in. He needed to get out of here and as he was he knew he wasn't going to be able to do it alone. This man scared him but he seemed to be trying. 

"Khan?" He tried then hedged when the larger man looked up from the PADD they had left them.

Kirk swallowed the lump in his throat. "Have you ever bonded anyone before?" He hated how brittle his voice sounded. 

"No, where I come from a bond is the same as a marriage. It is supposed to be for life." 

Again Kirk hesitated. "Can it be broken?" 

Kirk felt Khan's apprehension through the bond before he answered. "It is dangerous to try, but it can be done. Usually if a bond is able to form it is because two people are compatible. There is usually no reason for a bond to be broken. It causes a great deal of distress from both parties."

"Oh." Kirk lowered his eyes. 

There was a pause. "It's ok to feel scared James." Khan hadn't moved but Kirk could feel understanding and comfort flowing from him. 

"What's going to happen to me?" Kirk sniffed. He cursed and brushed the tears from his eyes. 

Khan made a move to stand but seemed to think better if it before asking,"Do you have a family?" 

Kirk sniffed. "My dad died before I was born and my mom left years ago. I doubt my step-father even knows I'm gone." 

That was a sad thought. Here he was on an alien vessel as a science experiment, would probably die before he escaped and no one cared. No one would miss him if, or rather, when he died.

"If you want to return to earth I will arrange it, but if you wanted I'm sure my crew would welcome you." 

Kirk sniffed again. "Do you have family?"

Khan smiled almost fondly and Kirk felt a different kind of warmness through the bond; a feeling of home and love; of hugs and time spent together. "My crew is my family and I need nothing else." Said Khan with a certainty and a ferocity. 

Kirk was able to look at him then. There was still a lot they needed to sort through but Kirk relaxed a little. This was a man who protected what was his and even though it may not have been intentional, Khan had made Kirk his. 

Khan was thankful for Kirk. It gave him somewhere to focus his energy. He distracted himself with taking care of James. He brought him water, prepared food for him and helped heal his wounds. He still sensed a great deal of fear flowing from the young man. He sent a constant stream of calm and safe through the bond. There was so much he wanted to say to him but how does one talk to their own accidental rape victim? 

He sighed and scratched his head. Time was one thing he had and was willing to give his mate.


	3. Chapter 3

Chapter 3  
Days passed and James's wounds healed. The scientists were reclusive but not non-existent. At first they tried drugging their food but after the first time Khan's system adapted to fight it off. Instead, they turned to periodically bursting through the door and shooting them both with sedatives before taking blood samples and doing other tests.

James went into a constant state of anxiety because of that (even though he would deny it). There was no way to determine when they would burst in and to James it felt like he was constantly under attack. Khan was trained to be calm in these situations. He reminded himself that his crew would find them, no matter what, but he still worried for the omega. He tried to distract him with chess or just talking but James stopped responding after awhile. James had also stopped sleeping and eating which also concerned Khan to no end. 

James was not a solider like Khan was. He wasn't built to be under this much stress and Khan knew he would crack soon. 

The next time the scientists burst in they broke pattern. When Khan woke up James wasn't in the room with him. "James? JAMES?" His alpha instincts kicked in. His mate was gone. His mate had been taken. He must protect his mate. Where was his mate? 

An hour he waited growing more and more anxious. It felt like an eternity, but finally FINALLY they returned with his conscious but blindfolded and shaken-looking omega. He snarled at them and snatched his mate away from them. 

He bundled James into his chest and blocked him away from them with his body. When they left he lifted James up and sat him on the bed. "Are you alright? Did they hurt you?" 

"N-no. They just in-injected me with s-something." 

"Do you know what it was?" 

"I-I don't know but I'm fre-freezing." 

"May I touch you? I'll try and warm you up."

James nodded and Khan bundled him up into his chest. It felt so good to hold him like this. 

"Why do you care?" James asked. "You don't know me. You didn't choose me. I'm not even an augment like you. Why do you take care of me? Why are you trying to be nice to me? I don't understand." 

He knew he was Khan's. He had made peace with that but he didn't know WHY. Kirk hoped feverishly it wasn't just out of a sense of responsibility, but really what else could the augment see in him? Since they had met he had done nothing but show weakness. He had cried and even had nightmares like a child. 

Khan contemplated his answer carefully. "I am not always a good man. I have done things I regret very deeply. You have seen my savagery, and yet I sense you are trying to forgive what in my mind is unforgivable. You make me want to believe that I can still be a good man. You have shown considerable strength even for an augment. Many men would crack in your position but I do not doubt in your resiliency. Once we get out of this wretched place you will allow this experience to make you a great man. A man I would be honoured to have as a mate." 

Kirk thought for a moment. He felt love and respect through their bond. So much he could nearly weep. Instead he reached up and kissed the augment gently. It was chaste but it meant so much. 

"Thank you my alpha." 

Khan nuzzled him. "I'll get us out if here. I promise."


	4. Chapter 4

Chapter 4  
It happened three more times. The scientists rushed in and Khan woke alone in the room. Only for them to return James to him an hour later under the effects of a new drug. 

The first time he was cold. The second time he returned extremely fabric sensitive and refused to touch anything except the bed covers. He even made Khan carry him to the bathroom because he claimed the carpet felt like needles on his feet. The third time he claimed he had terrible cramps in his stomach.  
The fourth time it happened was the worst and everything made sense; the scientists were trying to induce him into an early heat and had finally succeeded. 

The fourth day James was returned to him feeling feverish, but when he got close enough he could smell it on him. James had no idea what was happening to him. Omegas only went into heat every few months and only if they are bonded and Khan imagined from what he had told him that no one had taught James that important fact yet. 

"It hurts. It HURTS. Why does it hurt?" James whimpered. 

But pain only got worse. James was inconsolable. That was something else Khan betted no one told him; If an omega is bonded and goes into their first heat then they must mate or the omega could eventually die. 

Khan deliberated what to do. They weren't ready to have sex again. They've taken steps yes but were no where near close to trying again and especially not like this. Khan looked at his mate. James had curled around a pillow, his hands gripped so tightly his knuckles turned white. 

Khan eventually made a choice. "James come here." Khan sat on the bed and held James. The presence of his alpha should make the pain abate somewhat Khan hoped. 

James gasped. "What are you doing?" Khan was careful with his explanation. 

"James, you are in heat. Your first heat. Did anyone ever tell you what that means?"

Khan felt the exact moment Kirk panicked through the bond. 

"We have to do it again." James said all feelings of terror flooding him. 

"James listen–" "NO! DON'T TOUCH ME! Get away!" James fled to the corner pushing himself as far into the wall as he could manage. "NO! DON'T TOUCH ME!" He screamed, flailing desperately as Khan took hold of him.

"James calm down!" He urged. "James. Look at me." Kirk wasn't listening. He fought desperately to get out of Khan's grip and started hyperventilating. Panic gripped his chest like the first day he met Khan. His cries became omegan howls of distress and it broke Khan's heart. 

Khan had no choice. He spun Kirk around and pinned him against his chest before biting down into his shoulder. Kirk screamed and struggled for a moment before going limp. Panting, dizzy and shaking all over he asked "Wha-what did you do?" Khan mouthed the wound gently. "The saliva of bond mates has a calming effect. I'm trying to get you to relax. They drugged you. I know your body feels out of control and you're scared but you need to calm down." He hugged him and projected the deepest feelings of love and comfort in him to through the bond. "I love you my omega. I love you and we'll get through this. I promise." 

"My alpha....Please don't hurt me." He whispered the last part so quietly Khan barely heard. 

"James. Look at me." Khan urged. "I'll be gentle." He whispered. "I won't hurt you. The first time we did it I wasn't in control of myself and it was wrong. Sex isn't supposed to hurt. Just try to relax. If you're scared I will stop. I promise. Just try to relax. Shh. It's ok. It'll be alright. Let me make you feel good."

He lay him down on the bed and kissed him gently. He kept the pace slow and reassuring. James was anxious and shy but eventually he began tentatively kissing back. Khan deepened the kiss when he thought he was ready. Slow. He reminded himself. He needed to go slow.

He began removing his shirt with deft movements. James covered his face with his hands. "I don't want to do this." He said shakily. Khan stopped. "How can I help you get through this?" 

James was crying again. "Just-just keep talking. Let me know it's really you." 

"Alright." Khan began kissing him again. He couldn't mess this up. "James" he whispered. "Thank you for trusting me."

James still trembled and was tense but tilted his neck exposing his throat in a hesitant submission. Khan knew how difficult it must be for Kirk to be vulnerable here; knew what a gift it was. 

He licked and sucked all over his neck and worked his way down to his chest. "Am I the first to touch you like this James?" James whimpered. "The first to see you." He started taking off James's pants watching carefully in case he tired to stop him. 

There was no resistance as he took him in his mouth. James gasped and began running his fingers through Khan hair. Khan had taken lovers before and allowed himself a bit of pride. He was a very good lover when he wanted to be. 

James came quickly with a shudder and a series of harsh breaths. Khan hoped it would relax him for what happened next. 

He probed his entrance gently. It was wet with slick and Khan gently pressed his finger inside. James had his eyes closed and head turned and Khan felt barely contained terror through the bond. "Look at me James." He continued scissoring his fingers. "I love you." He kissed up his thighs. "I love you." When felt like James could accommodate him he lined himself up. "May I continue?" James nodded but continued to hide his face. Khan felt him disassociate through the bond; he was trying to think of something else and not the terror he was expecting from him. Khan let him. Kirk had been traumatized and he was asking a lot of him already. Khan looked into his eyes and saw terrifying blankness but at least he was relaxed. 

Khan thrust in gently and moved slowly. It was scandalously sensual. This was not animalistic or beastial as it had been the first time. He was careful. 

He moved James's hands and kissed him again and kissed him gently. Whispering he was beautiful and brave; that he was safe and nothing was going to hurt him. 

He focused on Kirk's pleasure first but he could feel his knot inflating. He thrust deep into James and groaned in satisfaction when they both came. They were tied together and would be for awhile yet. 

Khan collapsed onto James and held him tenderly. "Are you ok?" James still trembled and took a few seconds to respond. He began running his hands carefully over Khan as if he were placating a wild animal. "I'm ok. This is...I don't know what to do." He said shakily. 

"Just hold still and relax." Khan growled as another flow of pleasure went through him. 

Kirk stiffed at the feeling but relaxed after awhile. 

Khan felt a swell of relief in the bond. It was Kirk just feeling relieved he hadn't been torn apart this time. 

But Khan also felt a niggle of worry through the bond and poked at it. 

"What if I get pregnant?" Kirk asked.  
"Augments are sterile. You can't get pregnant from laying with one." That was done purposely by the engineers who designed augments in the first place. If you lost control of a superior race of people at least they couldn't reproduce to add to their numbers. 

Kirk nodded tiredly and dozed safely under his alpha.


	5. Chapter 5

Chapter 5

Days passed. After Kirk's heat the scientists bothered them less frequently and it allowed them to relax somewhat. The result was almost domestic if you subtracted the fact they spent most of the day in the apartment-cell. They touched a little more now but Kirk still struggled with more intimate aspects of the relationship. They would sleep curled up together at night and would have make out sessions but Kirk always pulled away before things went any further. Khan could sense his mate's frustration with himself. It still bothered him that Kirk was afraid of him but they were dealing. 

They spent their time playing chess until that got dull. They learned more about one another. In the close proximity it was difficult not to learn about one another. Khan spoke about his family often once he opened up. Kirk talked about the future. He wanted to be like his father. He wanted to be the captain of his own starship.

It wasn't ideal or expected but they had a functional relationship. 

However most of the time they were bored and cold. There wasn't much to do. 

Then there came a day where the scientists burst through the door with weapons and shot at Kirk. The shot missed him by a hair. Khan felt a rage bloom in him. No they were not taking his mate this time. He flipped up the table and threw it at them and snarled as they retreated. 

They didn't bother them again but Khan was feeling unsettled and uncharacteristically aggressive. He paced the room territorially.   
He growled low in his throat. Apprehension bloomed in the bond on Kirk's end. For some reason that set Khan off. 

He threw the dresser at the wall. His fists were shaking and his head was fuzzy with rage. All the pent up frustration and anger he felt and covered up over the past few weeks came out full force. 

"Khan stop!! What are you doing?!" 

He lashed out, nothing was safe. He tore up curtains, cupboards, the bed, even part of the floor. 

"No one touches you but me. You are mine." Khan barked.

A look of panic flashed across Kirk's face before he stepped forward carefully. The tension was thick and he chose his next move very carefully. He lowered his head submissively and moved to stand chest to chest with the alpha. Kirk put his head on Khan's chest. It was a simple gesture that meant 'I'm here'. 

It stopped Khan in his tracks. Khan's breaths came in shudders. His brain was starting to catch up with his body.

He pulled in an unsteady breath. "My apologies." He said; shocked at his own behaviour. "It seems as though I have lost my temper." He felt dizzy with the kickback of emotion. "Are you alright?"

Kirk turned his head. "Would you like to maybe sit down?" He said ignoring his question tellingly. 

"I feel as though that might be best." 

They curled up together. Khan was comforted by the smell of his mate. Kirk rubbed his back and the rage faded completely with the knowledge that his mate was safe and cared about him. They sat quietly for awhile. 

"Are you afraid of me?" Khan asked once he calmed down. Kirk shook his head. "I used to be but that was before I learned you're such a mush beneath that tough alpha exterior." 

"I believe you are mistaken about me being, as you say, a mush." He countered. 

"Are you seriously pouting? Don't worry. I won't tell anyone but in all seriousness, are you ok? I've never seen you so emotional before."

Khan felt shame at his lapse in control. "I have no idea. I've never felt so...threatened before. They were in my space. They were touching what wasn't theirs. I...snapped." Khan analyzed. 

"Is there something else? Homesick maybe?" 

Khan contemplated. "My crew was supposed to be here by now. I am...anxious that they haven't retrieved us yet but that shouldn't have resulted in such a break of conduct." 

"It happens. It's alright. I'm sure your crew is fine. Do you mind if I sleep? I'm not feeling all that great." Khan nodded and adjusted their position on the bed. Khan felt Kirk fall asleep. His breathing slowed and his body relaxed. It took him longer to achieve but Khan eventually followed him.   
\--------  
Khan woke up the next morning with a start. 

He hadn't been paying close enough attention. It shouldn't be possible but he smelled something unusual about his mate. 

Kirk was pregnant.

Khan grabbed Kirk without thinking and breathed deeply. It was his child. 

Khan thought it was too good to be true. Almost afraid to hope it was true. 

It explained everything. Their moods, Khan's desire to fiercely protect and his surplus of alpha hormones. 

He was going to be a father. He never thought it possible. He hugged a very confused half-asleep Kirk closer. 

"Khan? What's wrong? What are you doing?" 

Khan shook himself. Now was not the time to tell him. They weren't safe yet and this knowledge might scare him even more. 

Damn his crew where were they? 

"Khan?"   
"You need to trust me for the next little while. I can't give you more information in case they are listening but I may tell you to do something that may sound dangerous or unreasonable but I need you to do   
it regardless." 

Kirk's face hardened. "What are we talking about? What do you mean? I need to know what to expect." 

"I do not know myself but you have to trust me. Please James just trust me."


	6. Chapter 6

Chapter 6

Their salvation came a few days later with a racket to wake the dead. 

It sounded as if an army had infiltrated but when the noise reached the room there were only five augments. 

"Secure the rest of the area. Seize the computer's data and destroy everything else. You took much longer than expected what kept you?" Khan greeted. 

"We ran into some engine trouble when they attacked" a blond augment answered. 

"Was anyone else taken?"

"3 others sir. All dead." 

Khan looked distraught for a moment before reapply his captain mask. "Right. James this is Alex. Alex take him to the ship and take care of him until I get back."

Alex, a beta, caught wind of Kirk and his stone-faced expression looked stunned for a second. "Is he?-"

"That is not important at the moment. Get him back to the ship. Keep him safe at all costs. Bring him to the med bay. I want a full examination done."

"Khan, what's going on? Where are you going?" The thought of being separated from Khan to be left with more strangers sent a feeling of distress through him. 

"Go with him James." Khan snapped as he walked away from them. 

Kirk jolted at Khan's alpha tone.

Alex held out his hand politely and James took it. 

"This is Alex to the Vengeance, two to beam up." 

Alex said nothing as he escorted James through the ship. James was dazed by how fast things had happened. He was free? 

He felt weak and nauseous and it must have shown on his face because Alex slowed the pace somewhat. 

He was brought to the med bay as Khan instructed and he was introduced to a petite blond omega nurse whose name he'd already forgotten. 

"Can I get you anything? Are you hungry?" Alex asked. 

James shook his head. "Does anything hurt?" 

"No. I'm fine." He lied. He felt shaky and sick. 

Alex retrieved a blanket for him. Kirk hadn't realized he was cold. 

"Where is Khan?"

"He went to go retrieve the research left behind."

"Why? What is there that's so important?"

Alex sighed. "I don't know how much I'm allowed to tell you."

The blond omega lady came in and began giving him instructions; telling him to lay down, to breathe deeply and raise his hands. 

She took blood and urine samples, checked his eyes, ears and mouth. 

She told him they had been injecting him with heat inducers and that would explain his intense moods. She told him that they were dangerous and addictive and he would suffer though withdrawal for awhile and would have to stay in the med bay to be monitored. He sensed there was something they weren't telling him but his body felt exhausted. He wanted to be alone somewhere dark and sleep. 

The augments in the room seemed to notice this and escorted him to a smaller rest room filled with blankets and pillows and left him to himself. Alex told him he'd be outside if he needed anything. 

For the first time since he had been taken he was alone. 

\-------------------  
Khan returned covered in blood and smelling of rage. Alex stepped by his side. 

"Where is he?" 

"In the omega room. Safe. He's starting to nest."

"How's the baby?" 

"Baby is healthy. No foreseeable problems. "

"How is my mate?" 

"Withdrawal symptoms; they have been drugging him with heat inducers. He will experience nausea, dizziness, exhaustion, increased sensitivity. He will probably experience more severe symptoms tomorrow such as sweating, hysteria, headaches and temperature fluctuations. It explains his early nesting."

"Did you tell him?"

"No, I thought to leave that to you."

Khan paused. 

"I have missed you my friend."

Alex scoffed. "Perhaps your time away has made you sentimental. I do, however, think it is your best interest to let your mate know what he's in for but perhaps a shower first."

Khan smiled. "I'm going to be a father." 

"My congratulations sir." 

Then his face changed. "They took him from his planet and he's still so young. They drugged me so that I would mate with him. I raped him Alex. I raped him twice technically. There was no consent. I broke some of his bones." 

"I had wondered what changed your mind about taking a mate. I think you dwell in the past too much. From what I've seen he does care for you a great deal. Shower, go to him and sleep. You'll both feel better for it. I'll have your breakfast sent up to you."

"Thank you Alex."


	7. Chapter 7

Chapter 7

Khan entered the room and immediately smelt his pregnant mate. He was beautiful awake but unearthly when he was asleep. His face relaxed to make him look angelic. 

Kirk would sleep very deeply because of the heat inducer withdrawal. Khan felt conflicted at touching at first but began rubbing Kirk's belly. "Hello little one." He whispered. It was too soon to feel any movement but it sent a flutter of emotion to acknowledge the baby. 

Khan didn't know what he would do if Kirk decided to leave. The baby Kirk carried would be the future of augments. If they could reverse engineer how their captors managed to do it then Kirk was the most precious thing augments had. He was their chance for a future. 

He wanted to do the right thing and let Kirk go home if he wanted to but the baby was just too precious. He didn't want to make Kirk a captive again. He loved him. He loved taking care of him, loved his intelligence, his wit, his cockiness, his eyes, his grumpy snark in the morning, the face he made while playing chess or lost in thought. He didn't want to let him go but he didn't want to hurt him. 

He curled up into the bed with him and Kirk unconsciously nosed Khan's scent gland; seeking comfort from his alpha. He hoped Kirk wanted to stay. He wondered how he was going to tell Kirk about the baby. 

He kissed his forehead. "You mean so much to me." He prepared for a rough day tomorrow. 

\------------------  
The world was uneven and tumbled beneath him. 

"James? Did you fall down? Shhh. Hold still. Don't move yet." He was on the floor. How did he get here? His body trembled and it felt out of his control. 

"You're shaking. Are you scared James?" He couldn't answer.

"Can you speak? It's ok. You're going to be alright."

Everything spun and thoughts were slippery and fast moving. His breath shuddered in his lungs. 

"Just relax. Slow down. Let's get you back on the bed." Things got fuzzy for awhile. Strong hands flipped and lifted him. 

Someone was stroking his head. A voice spoke softly and it was putting him to sleep. 

"That's it. Go to sleep." 

Lucidity was tough. It felt like he was coming down from a bad high. He saw things. Spiders crawled across his skin and he clawed at them with his nails only to be stopped by unseen hands. Someone was screaming. 

"Is he alright?"

"I think he's a little freaked out. Here help me move him onto his side." 

"I'll hook him up to the IV. He needs to hydrate."

The world tilted and another blanket was placed over him and he shuddered. How was he unaware that he was cold? 

He was dragged into a furnace. Suddenly he was too warm. He squirmed but he was held tight.

"No James. You are too cold. Oh James. Please don't cry." Someone was rubbing his arm. "You're safe. It's ok." 

He was crying? His face was wet so maybe he was crying.

He slept again. Awake. Asleep. He couldn't tell anymore. Each time he woke the world came a little more into focus.   
It was the next morning before he felt fully cognizant of himself. 

"Well that wasn't so bad." He groaned. He stood up and felt dizzy but got dressed and made his way out the door. The nurse omega was there and noticed him with a bright "good morning. How are you feeling?" 

He flashed a smile he didn't really feel. "I'm alright. Uh-do you know where I could find a washroom?" 

It felt weird to be allowed to go places. He realized how much he had missed people; missed sound; missed wandering and exploring. He felt exhilaration and relief. He was alive! He had survived being experimented on. Survived being a captive.

He found the washroom and looked in the mirror. He didn't recognize himself. He was worn out. Lines were darker around his eyes and his stomach pooched out a little. His hair was longer and his beard had filled in to be scruffy. He needed to shower and shave. He needed to learn how to be a person again. He wanted his own room again. He wanted to own things again. He wanted to make his own food again. He felt like a ship without a tether. He needed to go home; needed to put himself back together. 

He got some strange looks as he headed back to the med bay. He felt nervous and exposed and walked a bit faster. The med bay wasn't ideal but it was at least safe. 

He turned in to see Khan talking to the nurse. Upon seeing him Khan smiled. "James. I have your room ready for you. I have arranged for some clothes and essentials to be brought to you." He turned to the nurse "Thank you Bella. There is none better than yourself."   
\----  
Kirk was very pleased to be clean again. His face was smooth again and he felt much better. He had used the shower and then had a bath in succession. His face was clean shaven and he felt more like a person. 

"James, there are some things we need to discuss." 

"Such as?" 

"Our relationship. I know you didn't choose me but I want to know what you want to do now that you are free. Do you wish to return to earth?" 

Kirk looked at Khan. Khan was the man who had seen him at his most vulnerable. He took care of him and loved him and Kirk didn't feel like he deserved any of it. It felt like a debt Kirk couldn't pay back. He didn't know how he felt. He felt so jumbled up inside. He loved this man but he felt afraid of losing his independence. While they were captured Kirk gave all the decisions to Khan. Now he wanted to learn how to be strong on his own again. Currently he felt unworthy of Khan's love. 

"Khan. I would like to go home for awhile. I need to figure myself out. It feels like I've forgotten who I am and I can't do anything until I sort myself out." 

Khan hesitated. Not knowing how to tell Kirk this. He took his hands in his own and drew strength from the bond. 

"James Tiberius Kirk. Listen to me and know that I love you. I would like you to be happy whatever you choose to do but there's something that you need to know." 

Khan took a deep breath. "You are pregnant with my child and the future of the augment race."

The blood in Kirk's veins froze and for a long time he couldn't process what had been said to him. 

"....I'm pregnant." 

"Yes. Your scent has changed and the nurse confirmed it. Forgive me. I should have told you sooner but I wasn't sure and I didn't want to be wrong." 

"I thought you said augments were sterile?!"

"I thought so too but they injected us with something that reversed the process. The baby you have inside will allow augments to have families-"  
Kirk stopped listening. He suddenly felt numb. It was too much. He didn't feel anything. He lowered his head into his knees and wrapped his arms around himself in self-comfort. 

"Kirk?"

"I can't do this anymore." He whispered. "Get out." 

"James I-" "GET OUT!!" Kirk was shaking. "Please." He held his head. He thought Khan was going to push him. He was fully prepared to lash out at Khan but Khan stood and left without a word.

Kirk threw himself into a full blown emotional breakdown. He screamed, he cried, he tore up the bedroom. All the pain, fear and stress he had saved up the past few months came spilling from his soul in a torrent. He didn't choose any of this. He was no one. Why did he have to go through this? Why did these things keep happening to him? He couldn't handle it. Were they even going to let him go home? He was terrified. He felt trapped.

He yanked his hair and clawed at his arms. He didn't even try to stop or quiet himself. He shouted hateful, things at himself, at Khan, at the universe. He was lost. He was alone. And he was so, so very tired.


	8. Chapter 8

Chapter 8

Khan went to see Alex. Alex was his best friend since they were teenagers. Alex was his opposite and his equal and at first they hated each other until they had a massive fight that resulted in both of them breaking several of the other's bones. From that day forward they realized they respected the other's strength and were inseparable. 

He needed Alex's strength right now since he didn't trust his own. He was out of his depth. The bond in his head was screaming at him. It made him dizzy and sick. He had to fight himself not to run back to his mate. He stumbled into Alex's room disorientated and nauseas. 

"I need a drink." His hands were shaking and his head threatened to split open. 

"I take it telling him didn't go well." Alex got up and poured them both bourbon. Khan downed it in a single gulp. "He hates me." 

Alex snorted. "You sound like a lovesick teenager. Perhaps I should have been captain after all if this is all it takes to down you."

That actually made Khan smirk despite his terrible mood. "Get off it. We both know you hate people too much to stand being captain." Khan frowned. "I can feel him through the bond. I-I think I broke him." 

Alex nursed his own drink. "You give yourself too much credit. That young man has been through so much that anything at all at this point would have sent him over. You've broken nothing."

"Then why can I hear him screaming in my head?" 

"He'll pull through. He's bloody terrified. Who wouldn't be after his ordeal? This is healthy for him right now. This is him coping with what has happened to him." Alex sighed. "This is why I'll never take a mate. Too much drama." 

"What do I do Alex? You know as well as I do that baby is our future. I can't just let him go. What has the research told you?"

"We are making process. We may be able to replicate the process but it needs a little more time to say for sure."

"I don't want to let him go. I love him Alex. I never thought I could be a good man after what I've done. My hands are black with blood and yet I feel redeemed when I am with him. I love him and our child. I never thought I'd be a father and now I found myself wanting it more than anything." 

"You are drunk." Alex stated plainly sipping his own drink. 

"But that doesn't make it any less true." Khan suddenly felt overwhelmingly tired through the bond and from his own body. 

Alex noticed and scoffed. "Another reason I'll never mate. They'll kick you out of your own bed. I'll set you up the futon." 

"Bless your bleeding heart." Khan mumbled. 

"Only heart I have is in a jar on my desk. Get up. Move. Bloody captain my foot. More akin to a drunken frat boy."

**Author's Note:**

> Psst. If you liked it could you leave a kudos? Just a little one (or a big if you really want).


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